chr8-27397634-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_173176.3(PTK2B):c.50G>A(p.Arg17His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,614,092 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R17C) has been classified as Uncertain significance.
Frequency
Consequence
NM_173176.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTK2B | NM_173176.3 | c.50G>A | p.Arg17His | missense_variant | 2/31 | ENST00000346049.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTK2B | ENST00000346049.10 | c.50G>A | p.Arg17His | missense_variant | 2/31 | 1 | NM_173176.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152232Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251312Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135800
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461860Hom.: 0 Cov.: 64 AF XY: 0.0000124 AC XY: 9AN XY: 727222
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152232Hom.: 1 Cov.: 34 AF XY: 0.0000672 AC XY: 5AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | The c.50G>A (p.R17H) alteration is located in exon 7 (coding exon 1) of the PTK2B gene. This alteration results from a G to A substitution at nucleotide position 50, causing the arginine (R) at amino acid position 17 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at